Hi David, I was just pondering the same thing. From reading the source code, the 'samtools depth' -l argument seems to be the minimum mapped read length (which is calculated from the CIGAR string).
I have no idea what 'minQLen' was short for, unless the Q was a typo? My proposed change to samtools is here: https://github.com/samtools/samtools/pull/321 Peter On Thu, Mar 6, 2014 at 9:22 AM, David Garfield <david.garfi...@embl.de> wrote: > Good morning, > > I have a very basic question: With samtools 'depth', to what does the '-l' > option (minQLen) refer? > I'm doing some basic accounting with respect to base coverage in a set of bam > files, and I would like to know what options I have for filtering coverage by > quality. > > Many thanks, > > David ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
